Mihail Iotov - Academia.edu (original) (raw)
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Papers by Mihail Iotov
The goals of this research are twofold: First, to develop methods and tools for studying problems... more The goals of this research are twofold: First, to develop methods and tools for studying problems in chemistry, material science and biology, as well as accurate prediction of the properties of structures and materials of importance to those fields. Second, use those tools to apply the methods to practical problems. In terms of methodology development this thesis focuses on two topics: One: Development of a massively parallel computer program to perform electronic, atomic, molecular levels simulations of problems in chemistry, material science and biology. This computer program uses existing and emerging hardware platforms and parallel tools and is based on decades long research in computer modeling and algorithms. We report on that development in Chapter 3. Two: Development of tools for Molecular Dynamics simulation and methods and tools for course-grained meso-scale modeling of transport properties and especially diffusion of gas penetrants in polymers. We have formulated a new me...
Computational and Theoretical Polymer Science, 2001
Advances in theory and methods are making it practical to consider fully ®rst principles (de novo... more Advances in theory and methods are making it practical to consider fully ®rst principles (de novo) predictions of structures, properties and processes for organic materials. However, despite the progress there remains an enormous challenge in bridging the vast range of distances and time scales between de novo atomistic simulations and the quantitative continuum models for the macroscopic systems essential in industrial design and operations. Recent advances relevant to such developments include: quantum chemistry including continuum solvation and force ®eld embedding, de novo force ®elds to describe phase transitions, molecular dynamics (MD) including continuum solvent, non equilibrium MD for rheology and thermal conductivity and mesoscale simulations. To provide some¯avor for the opportunities we will illustrate some of the progress and challenges by summarizing some recent developments in methods and their applications to polymers and biopolymers. Four different topics will be covered: (1) hierarchical modeling approach applied to modeling olfactory receptors, (2) stabilization of leucine zipper coils by introduction of tri¯uoroleucine, (3) modeling response of polymers sensors for electronic nose, and (4) diffusion of gases in amorphous polymers.
2007 International Conference on Field Programmable Logic and Applications, 2007
Structured ASICs have recently emerged as a midway between cell-based ASICs with high NRE costs a... more Structured ASICs have recently emerged as a midway between cell-based ASICs with high NRE costs and FPGAs with high unit costs. Though the structured ASIC fabric attacks mask and other fixed cost it does not solve verification, particularly physical verification issues with ASICs or logic errors missed by simulation which would require re-spins. These can be avoided by testing in-system with an FPGA and migrating the FPGA design to a closely coupled structured ASIC fabric. Here we describe a practical methodology for a fast, pushbutton, and thorough verification approach tying an FPGA prototype to a matching structured-ASIC implementation for cost-reduction. Our focus is the equivalence verification between the respective revisions of a design, including netlist, compiler settings, macro-block parameters, timing constraints, pin layout and resource count.
We propose a method for studying diffusion in amorphous structures based on biased random walk in... more We propose a method for studying diffusion in amorphous structures based on biased random walk in the free volume extracted from a polymer ("the Monte Carlo Void Method .") We analyze a number of simple free volume structures not derived from realistic polymers and show that the biased random walk method is offering intuitively realistic description of the particle motion and present a framework for computing diffusion coefficents.
Letters in Mathematical Physics, 1991
A compact form for the universalR-matrix of Uq(sln) is derived and illustrated by simple applicat... more A compact form for the universalR-matrix of Uq(sln) is derived and illustrated by simple applications.
Journal of Computational Chemistry, 1997
Ž. We describe the implementation of the cell multipole method CMM in a Ž. Ž. complete molecular ... more Ž. We describe the implementation of the cell multipole method CMM in a Ž. Ž. complete molecular dynamics MD simulation program MPSim for massively parallel supercomputers. Tests are made of how the program scales with size Ž. Ž. linearly and with number of CPUs nearly linearly in applications involving up to 10 7 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry.
The goals of this research are twofold: First, to develop methods and tools for studying problems... more The goals of this research are twofold: First, to develop methods and tools for studying problems in chemistry, material science and biology, as well as accurate prediction of the properties of structures and materials of importance to those fields. Second, use those tools to apply the methods to practical problems. In terms of methodology development this thesis focuses on two topics: One: Development of a massively parallel computer program to perform electronic, atomic, molecular levels simulations of problems in chemistry, material science and biology. This computer program uses existing and emerging hardware platforms and parallel tools and is based on decades long research in computer modeling and algorithms. We report on that development in Chapter 3. Two: Development of tools for Molecular Dynamics simulation and methods and tools for course-grained meso-scale modeling of transport properties and especially diffusion of gas penetrants in polymers. We have formulated a new me...
Computational and Theoretical Polymer Science, 2001
Advances in theory and methods are making it practical to consider fully ®rst principles (de novo... more Advances in theory and methods are making it practical to consider fully ®rst principles (de novo) predictions of structures, properties and processes for organic materials. However, despite the progress there remains an enormous challenge in bridging the vast range of distances and time scales between de novo atomistic simulations and the quantitative continuum models for the macroscopic systems essential in industrial design and operations. Recent advances relevant to such developments include: quantum chemistry including continuum solvation and force ®eld embedding, de novo force ®elds to describe phase transitions, molecular dynamics (MD) including continuum solvent, non equilibrium MD for rheology and thermal conductivity and mesoscale simulations. To provide some¯avor for the opportunities we will illustrate some of the progress and challenges by summarizing some recent developments in methods and their applications to polymers and biopolymers. Four different topics will be covered: (1) hierarchical modeling approach applied to modeling olfactory receptors, (2) stabilization of leucine zipper coils by introduction of tri¯uoroleucine, (3) modeling response of polymers sensors for electronic nose, and (4) diffusion of gases in amorphous polymers.
2007 International Conference on Field Programmable Logic and Applications, 2007
Structured ASICs have recently emerged as a midway between cell-based ASICs with high NRE costs a... more Structured ASICs have recently emerged as a midway between cell-based ASICs with high NRE costs and FPGAs with high unit costs. Though the structured ASIC fabric attacks mask and other fixed cost it does not solve verification, particularly physical verification issues with ASICs or logic errors missed by simulation which would require re-spins. These can be avoided by testing in-system with an FPGA and migrating the FPGA design to a closely coupled structured ASIC fabric. Here we describe a practical methodology for a fast, pushbutton, and thorough verification approach tying an FPGA prototype to a matching structured-ASIC implementation for cost-reduction. Our focus is the equivalence verification between the respective revisions of a design, including netlist, compiler settings, macro-block parameters, timing constraints, pin layout and resource count.
We propose a method for studying diffusion in amorphous structures based on biased random walk in... more We propose a method for studying diffusion in amorphous structures based on biased random walk in the free volume extracted from a polymer ("the Monte Carlo Void Method .") We analyze a number of simple free volume structures not derived from realistic polymers and show that the biased random walk method is offering intuitively realistic description of the particle motion and present a framework for computing diffusion coefficents.
Letters in Mathematical Physics, 1991
A compact form for the universalR-matrix of Uq(sln) is derived and illustrated by simple applicat... more A compact form for the universalR-matrix of Uq(sln) is derived and illustrated by simple applications.
Journal of Computational Chemistry, 1997
Ž. We describe the implementation of the cell multipole method CMM in a Ž. Ž. complete molecular ... more Ž. We describe the implementation of the cell multipole method CMM in a Ž. Ž. complete molecular dynamics MD simulation program MPSim for massively parallel supercomputers. Tests are made of how the program scales with size Ž. Ž. linearly and with number of CPUs nearly linearly in applications involving up to 10 7 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry.